Association of bacterial infection traits with genetic variation at candidate genes for porcine disease resistance

2004 ◽  
Author(s):  
Christopher K. Tuggle ◽  
Xian-wei Shi ◽  
Lena Marklund ◽  
Amber Stumbaugh ◽  
Thomas J. Stabel ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Disease Resistance ◽  
Bacterial Infection ◽  
Candidate Genes

scholarly journals Genetic polymorphism of candidate genes in pig meat production

2011 ◽  
pp. 37-40
Author(s):  
Zuzana Lieskovská ◽  
Anton Kováčik ◽  
Anna Trakovická
Keyword(s):  
Genetic Variation ◽  
Genetic Polymorphism ◽  
Candidate Genes ◽  
Fat Content ◽  
Meat Production ◽  
Lepr Gene ◽  
Pcr Rflp ◽  
Pig Meat

H-FABP, LEPR and MC5R genes were suggested as candidate genes for fat content in pig meat. The aim of this study was to detect genetic variation in the porcine H-FABP, LEPR and MC5R genes by PCR-RFLP method in a group of pigs. Genotyping of pigs was done by PCRRFLP methods. We identified three genotypes in the set of pigs, HH (0.504), Hh (0.412) and hh (0.084) for H-FABP (HinfI). Allele H showed higher frequency than allele h (0.710 vs. 0.290). Three genotypes were identified for the H-FABP (HaeIII) gene (DD - 0.194, Dd - 0.494, dd - 0.312). The allele D (0.441) showed slightly lower frequency than allele d (0.559). All three genotypes were identified for LEPR (HpaII) in the group of pigs (AA – 0.137, AB - 0.314, BB – 0.549). Higher frequency of LEPR gene was confirmed for allele B (0.706), as compared with allele A (0.294). We identified two genotypes for MC5R (BsaHI) in the group of pigs (AA - 0.348 and AG - 0.652), genotype GG was not found. As conforms with genotype structure, we recognize a higher frequency of allele A (0.674) as compared with allele G (0.326). 

scholarly journals Genome-Wide Association Study and QTL Mapping Reveal Genomic Loci Associated with Fusarium Ear Rot Resistance in Tropical Maize Germplasm

2016 ◽  
Vol 6 (12) ◽  
pp. 3803-3815 ◽  
Author(s):  
Jiafa Chen ◽  
Rosemary Shrestha ◽  
Junqiang Ding ◽  
Hongjian Zheng ◽  
Chunhua Mu ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Association Study ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Physical Map ◽  
Genome Wide Association ◽  
Fusarium Ear Rot ◽  
Ear Rot ◽  
Tropical Maize ◽  
Genome Wide

Abstract Fusarium ear rot (FER) incited by Fusarium verticillioides is a major disease of maize that reduces grain quality globally. Host resistance is the most suitable strategy for managing the disease. We report the results of genome-wide association study (GWAS) to detect alleles associated with increased resistance to FER in a set of 818 tropical maize inbred lines evaluated in three environments. Association tests performed using 43,424 single-nucleotide polymorphic (SNPs) markers identified 45 SNPs and 15 haplotypes that were significantly associated with FER resistance. Each associated SNP locus had relatively small additive effects on disease resistance and accounted for 1–4% of trait variation. These SNPs and haplotypes were located within or adjacent to 38 candidate genes, 21 of which were candidate genes associated with plant tolerance to stresses, including disease resistance. Linkage mapping in four biparental populations to validate GWAS results identified 15 quantitative trait loci (QTL) associated with F. verticillioides resistance. Integration of GWAS and QTL to the maize physical map showed eight colocated loci on chromosomes 2, 3, 4, 5, 9, and 10. QTL on chromosomes 2 and 9 are new. These results reveal that FER resistance is a complex trait that is conditioned by multiple genes with minor effects. The value of selection on identified markers for improving FER resistance is limited; rather, selection to combine small effect resistance alleles combined with genomic selection for polygenic background for both the target and general adaptation traits might be fruitful for increasing FER resistance in maize.

scholarly journals Contrasting genetic variation and positive selection followed the divergence of NBS-encoding genes in Asian and European pears

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Manyi Sun ◽  
Mingyue Zhang ◽  
Jugpreet Singh ◽  
Bobo Song ◽  
Zikai Tang ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Disease Resistance ◽  
Positive Selection ◽  
Gene Family ◽  
Selection Pressure ◽  
Black Spot ◽  
Orthologous Gene ◽  
European Pear ◽  
Encoding Gene ◽  
Encoding Genes

Abstract Background The NBS disease-related gene family coordinates the inherent immune system in plants in response to pathogen infections. Previous studies have identified NBS-encoding genes in Pyrus bretschneideri (‘Dangshansuli’, an Asian pear) and Pyrus communis (‘Bartlett’, a European pear) genomes, but the patterns of genetic variation and selection pressure on these genes during pear domestication have remained unsolved. Results In this study, 338 and 412 NBS-encoding genes were identified from Asian and European pear genomes. This difference between the two pear species was the result of proximal duplications. About 15.79% orthologous gene pairs had Ka/Ks ratio more than one, indicating two pear species undergo strong positive selection after the divergence of Asian and European pear. We identified 21 and 15 NBS-encoding genes under fire blight and black spot disease-related QTL, respectively, suggesting their importance in disease resistance. Domestication caused decreased nucleotide diversity across NBS genes in Asian cultivars (cultivated 6.23E-03; wild 6.47E-03), but opposite trend (cultivated 6.48E-03; wild 5.91E-03) appeared in European pears. Many NBS-encoding coding regions showed Ka/Ks ratio of greater than 1, indicating the role of positive selection in shaping diversity of NBS-encoding genes in pear. Furthermore, we detected 295 and 122 significantly different SNPs between wild and domesticated accessions in Asian and European pear populations. Two NBS genes (Pbr025269.1 and Pbr019876.1) with significantly different SNPs showed >5x upregulation between wild and cultivated pear accessions, and > 2x upregulation in Pyrus calleryana after inoculation with Alternaria alternata. We propose that positively selected and significantly different SNPs of an NBS-encoding gene (Pbr025269.1) regulate gene expression differences in the wild and cultivated groups, which may affect resistance in pear against A. alternata. Conclusion Proximal duplication mainly led to the different number of NBS-encoding genes in P. bretschneideri and P. communis genomes. The patterns of genetic diversity and positive selection pressure differed between Asian and European pear populations, most likely due to their independent domestication events. This analysis helps us understand the evolution, diversity, and selection pressure in the NBS-encoding gene family in Asian and European populations, and provides opportunities to study mechanisms of disease resistance in pear.

scholarly journals Haplotype Block Analysis Reveals Candidate Genes and QTLs for Meat Quality and Disease Resistance in Chinese Jiangquhai Pig Breed

2020 ◽  
Vol 11 ◽  
Author(s):  
Favour Oluwapelumi Oyelami ◽  
Qingbo Zhao ◽  
Zhong Xu ◽  
Zhe Zhang ◽  
Hao Sun ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Candidate Genes ◽  
Meat Quality ◽  
Haplotype Block

scholarly journals A PAI-1 (SERPINE1) polymorphism predicts osteonecrosis in children with acute lymphoblastic leukemia: a report from the Children's Oncology Group

Blood ◽  
2008 ◽  
Vol 111 (9) ◽  
pp. 4496-4499 ◽  
Author(s):  
Deborah French ◽  
Leo H. Hamilton ◽  
Leonard A. Mattano ◽  
Harland N. Sather ◽  
Meenakshi Devidas ◽  
...  
Keyword(s):  
Risk Factors ◽  
Genetic Variation ◽  
Acute Lymphoblastic Leukemia ◽  
Candidate Genes ◽  
Odds Ratio ◽  
Lymphoblastic Leukemia ◽  
Serum Levels ◽  
Oncology Group ◽  
Frequent Complication ◽  
Pai 1

Abstract As glucocorticoid use increased in acute lymphoblastic leukemia, osteonecrosis became an increasingly frequent complication. Besides increased age, host risk factors are poorly defined. We tested whether 12 polymorphisms were associated with osteonecrosis among patients 10 years and older treated on the CCG1882 protocol. Candidate genes (TYMS, MTHFR, ABCB1, BGLAP, ACP5, LRP5, ESR1, PAI-1, VDR, PTH, and PTHR) were chosen based on putative mechanisms underlying osteonecrosis risk. All children received dexamethasone, with doses varying by treatment arm. A PAI-1 polymorphism (rs6092) was associated with risk of osteonecrosis in univariate (P = .002; odds ratio = 2.79) and multivariate (P = .002; odds ratio = 2.89) analyses (adjusting for gender, age, and treatment arm). Overall, 21 of 78 (26.9%) children with PAI-1 GA/AA genotypes, versus 25 of 214 (11.7%) children with GG genotype, developed osteonecrosis. PAI-1 polymorphisms and PAI-1 serum levels have previously been associated with thrombosis. We conclude that PAI-1 genetic variation may contribute to risk of osteonecrosis.

scholarly journals Natural Genetic Variation and Candidate Genes for Morphological Traits in Drosophila melanogaster

PLoS ONE ◽  
2016 ◽  
Vol 11 (7) ◽  
pp. e0160069 ◽  
Author(s):  
Valeria Paula Carreira ◽  
Julián Mensch ◽  
Esteban Hasson ◽  
Juan José Fanara
Keyword(s):  
Drosophila Melanogaster ◽  
Genetic Variation ◽  
Candidate Genes ◽  
Morphological Traits ◽  
Natural Genetic Variation

scholarly journals Genetic architecture of natural variation in visual senescence in Drosophila

2016 ◽  
Vol 113 (43) ◽  
pp. E6620-E6629 ◽  
Author(s):  
Mary Anna Carbone ◽  
Akihiko Yamamoto ◽  
Wen Huang ◽  
Rachel A. Lyman ◽  
Tess Brune Meadors ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Genetic Variation ◽  
Life Span ◽  
Candidate Genes ◽  
Natural Variation ◽  
Genetic Basis ◽  
Nervous System Development ◽  
Interindividual Variation ◽  
Human Populations ◽  
Age Dependent

Senescence, i.e., functional decline with age, is a major determinant of health span in a rapidly aging population, but the genetic basis of interindividual variation in senescence remains largely unknown. Visual decline and age-related eye disorders are common manifestations of senescence, but disentangling age-dependent visual decline in human populations is challenging due to inability to control genetic background and variation in histories of environmental exposures. We assessed the genetic basis of natural variation in visual senescence by measuring age-dependent decline in phototaxis using Drosophila melanogaster as a genetic model system. We quantified phototaxis at 1, 2, and 4 wk of age in the sequenced, inbred lines of the Drosophila melanogaster Genetic Reference Panel (DGRP) and found an average decline in phototaxis with age. We observed significant genetic variation for phototaxis at each age and significant genetic variation in senescence of phototaxis that is only partly correlated with phototaxis. Genome-wide association analyses in the DGRP and a DGRP-derived outbred, advanced intercross population identified candidate genes and genetic networks associated with eye and nervous system development and function, including seven genes with human orthologs previously associated with eye diseases. Ninety percent of candidate genes were functionally validated with targeted RNAi-mediated suppression of gene expression. Absence of candidate genes previously implicated with longevity indicates physiological systems may undergo senescence independent of organismal life span. Furthermore, we show that genes that shape early developmental processes also contribute to senescence, demonstrating that senescence is part of a genetic continuum that acts throughout the life span.

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